metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis

• DOI: 10.1016/j.mcpro.2024.100840
• Publication Date: 2024-09-13T16:49:06Z
• Authors: Yingying Sun; Ziyuan Xing; Shuang Liang; Zelei Miao; Lai-bao Zhuo; Wenhao Jiang; Hui Zhao; Huanhuan Gao; Yuting Xie; Yan Zhou; Liang Yue; Xue Cai; Yu-ming Chen; Ju-Sheng Zheng; Tiannan Guo
• Keywords: Metaproteomics

Analysis of large-scale data-independent acquisition mass spectrometry (DIA-MS) metaproteomics data remains a computational challenge. Here, we present pipeline called metaExpertPro for analysis. This encompasses spectral library generation using data-dependent MS (DDA-MS), protein identification and quantification DIA-MS, functional taxonomic annotation, as well quantitative matrix both microbiota hosts. By integrating FragPipe DIA-NN, offers compatibility with Orbitrap timsTOF instruments. To evaluate the depth accuracy quantification, conducted extensive assessments human fecal samples benchmark tests. Performance tests on indicated that quantified an average 45,000 peptides in 60-minute diaPASEF injection. Notably, outperformed three existing software tools by characterizing higher number proteins. Importantly, maintained low factual false discovery rate (FDR) approximately 5% groups across four Applying filter five per genus, achieved relatively high (F-score = 0.67-0.90) genus diversity showed correlation (r